public Graph createGraph(Clustering[] clusts) {
Clustering c = clusts[0];
// total number of items
int n = c.instancesCount();
Graph graph = new AdjListGraph();
Object2LongOpenHashMap<Instance> mapping = new Object2LongOpenHashMap();
Instance a, b;
Node na, nb;
// cluster membership
int ca, cb;
int x = 0;
Edge edge;
// accumulate evidence
for (Clustering clust : clusts) {
System.out.println("reducing " + (x++));
for (int i = 1; i < n; i++) {
a = clust.instance(i);
na = fetchNode(graph, mapping, a);
ca = clust.assignedCluster(a.getIndex());
for (int j = 0; j < i; j++) {
b = clust.instance(j);
nb = fetchNode(graph, mapping, b);
// for each pair of instances check if placed in the same cluster
cb = clust.assignedCluster(b.getIndex());
if (ca == cb) {
edge = graph.getEdge(na, nb);
// check if exists
if (edge == null) {
edge = graph.getFactory().newEdge(na, nb, 0, 0, false);
graph.addEdge(edge);
}
// increase weight by 1
edge.setWeight(edge.getWeight() + 1.0);
}
}
}
}
return graph;
}
@Override
public String runMetis(Graph graph, int k, Props params) {
long current = System.currentTimeMillis();
File file = new File("inputGraph-" + current);
String filename = file.getName();
Process p;
try {
graph.hMetisExport(file, false);
if (metisFile == null) {
// fetch the file just once
metisFile = getBinary();
System.out.println("metis path: " + metisFile.getAbsolutePath());
}
// run metis
String space = " ";
StringBuilder sb = new StringBuilder(metisFile.getAbsolutePath());
sb.append(" ")
.append(filename)
.append(" ")
.append(String.valueOf(k))
.append(space)
.append("-ufactor=")
.append(String.valueOf(params.getDouble(UFACTOR, 5.0)))
.append(space)
.append("-nruns=")
.append(String.valueOf(params.getInt(NRUNS, 10)))
.append(space)
.append("-ptype=")
.append(String.valueOf(params.get(PTYPE, "rb")))
.append(space)
.append("-otype=")
.append(String.valueOf(params.get(OTYPE, "cut")))
.append(space);
if (params.containsKey(CTYPE)) {
sb.append("-ctype=").append(params.get(CTYPE)).append(space);
}
if (params.containsKey(RTYPE)) {
sb.append("-rtype=").append(params.get(RTYPE)).append(space);
}
// sb.append(String.valueOf(vcycle)).append(space);
p = Runtime.getRuntime().exec(sb.toString());
p.waitFor();
if (debug) {
System.out.println("cmd: " + sb.toString());
System.out.println("exit code: " + p.exitValue());
if (p.exitValue() != 1) {
// System.out.println(ExtBinHelper.readFile(file));
}
helper.readStdout(p);
helper.readStderr(p);
}
file.delete();
} catch (FileNotFoundException | UnsupportedEncodingException ex) {
Exceptions.printStackTrace(ex);
} catch (IOException | InterruptedException ex) {
Exceptions.printStackTrace(ex);
}
return filename;
}
private Node createNode(Graph g, Object2LongOpenHashMap<Instance> mapping, Instance inst) {
Node node = g.getFactory().newNode(inst);
mapping.put(inst, node.getId());
g.addNode(node);
return node;
}
private Node fetchNode(Graph g, Object2LongOpenHashMap<Instance> mapping, Instance inst) {
if (mapping.containsKey(inst)) {
return g.getNode(mapping.getLong(inst));
}
return createNode(g, mapping, inst);
}
@Override
public Clustering<E, C> reduce(
Clustering[] clusts, Algorithm<E, C> alg, ColorGenerator cg, Props props) {
Graph graph = createGraph(clusts);
// degree of freedom
double df;
double w, attain;
EdgeIterable neigh;
PriorityQueue<DoubleElem> pq = new PriorityQueue<>(graph.getNodeCount());
DoubleElem<Node> elem;
// for each node compute attainment score
for (Node node : graph.getNodes()) {
neigh = graph.getEdges(node);
df = neigh.size();
w = 0.0;
for (Edge ne : neigh) {
w += ne.getWeight();
}
attain = w / df;
elem = new DoubleElem<>(node, attain);
pq.add(elem);
}
// number of clusters is just a hint
int k = props.getInt(KMeans.K, 5);
double relax = props.getDouble(RELAX, 0.5);
Clustering<E, C> result = new ClusterList(k);
Dataset<? extends Instance> dataset = clusts[0].getLookup().lookup(Dataset.class);
result.lookupAdd(dataset);
ObjectOpenHashSet<Node> blacklist = new ObjectOpenHashSet();
Node node, other;
Cluster curr;
double maxW;
while (!pq.isEmpty()) {
elem = pq.poll();
node = elem.getElem();
if (!blacklist.contains(node)) {
blacklist.add(node);
curr = result.createCluster();
if (cg != null) {
curr.setColor(cg.next());
}
curr.add(node.getInstance());
EdgeIterable iter = graph.getEdges(node);
maxW = -1;
for (Edge ne : iter) {
if (ne.getWeight() > maxW) {
maxW = ne.getWeight();
}
}
// add immediate neighbours with max weight to same cluster
if (maxW >= 0.0) {
for (Edge ne : iter) {
// when relax set to 0.0, only items with maximum weight
// will be added to the same cluster
w = ne.getWeight() + relax * ne.getWeight();
if (w >= maxW) {
if (!node.equals(ne.getSource())) {
other = ne.getSource();
} else {
other = ne.getTarget();
}
if (!blacklist.contains(other)) {
curr.add(other.getInstance());
blacklist.add(other);
}
}
}
}
}
}
// TODO merge some clusters
return result;
}